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modified citation info for Lauterbur et al. (2023) in docs
Implemented PhoSin species (Vaquita). First version (before QC)
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| """ | ||
| Catalog definitions for PhoSin (Ensembl ID='phocoena_sinus') | ||
| """ | ||
| from . import species # noqa: F401 |
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| # File autogenerated from Ensembl REST API. Do not edit. | ||
| data = { | ||
| "assembly_accession": "GCA_008692025.1", | ||
| "assembly_name": "mPhoSin1.pri", | ||
| "chromosomes": { | ||
| "1": {"length": 185845356, "synonyms": []}, | ||
| "2": {"length": 178563925, "synonyms": []}, | ||
| "3": {"length": 174291665, "synonyms": []}, | ||
| "4": {"length": 146127150, "synonyms": []}, | ||
| "5": {"length": 139762554, "synonyms": []}, | ||
| "6": {"length": 115952311, "synonyms": []}, | ||
| "7": {"length": 115469292, "synonyms": []}, | ||
| "8": {"length": 110408561, "synonyms": []}, | ||
| "9": {"length": 106736052, "synonyms": []}, | ||
| "10": {"length": 102828027, "synonyms": []}, | ||
| "11": {"length": 104118372, "synonyms": []}, | ||
| "12": {"length": 90399378, "synonyms": []}, | ||
| "13": {"length": 90400161, "synonyms": []}, | ||
| "14": {"length": 89762611, "synonyms": []}, | ||
| "15": {"length": 88287594, "synonyms": []}, | ||
| "16": {"length": 85252673, "synonyms": []}, | ||
| "17": {"length": 79603858, "synonyms": []}, | ||
| "18": {"length": 79885847, "synonyms": []}, | ||
| "19": {"length": 59501331, "synonyms": []}, | ||
| "20": {"length": 58878645, "synonyms": []}, | ||
| "21": {"length": 35802323, "synonyms": []}, | ||
| "X": {"length": 131664873, "synonyms": []}, | ||
| }, | ||
| } |
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| import stdpopsim | ||
|
|
||
| from . import genome_data | ||
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|
||
| _species_ploidy = 2 | ||
| _ploidy = { | ||
| "1": _species_ploidy, | ||
| "2": _species_ploidy, | ||
| "3": _species_ploidy, | ||
| "4": _species_ploidy, | ||
| "5": _species_ploidy, | ||
| "6": _species_ploidy, | ||
| "7": _species_ploidy, | ||
| "8": _species_ploidy, | ||
| "9": _species_ploidy, | ||
| "10": _species_ploidy, | ||
| "11": _species_ploidy, | ||
| "12": _species_ploidy, | ||
| "13": _species_ploidy, | ||
| "14": _species_ploidy, | ||
| "15": _species_ploidy, | ||
| "16": _species_ploidy, | ||
| "17": _species_ploidy, | ||
| "18": _species_ploidy, | ||
| "19": _species_ploidy, | ||
| "20": _species_ploidy, | ||
| "21": _species_ploidy, | ||
| "X": _species_ploidy, | ||
| } | ||
|
|
||
| # There is no good justificaiton for this value for now. | ||
| # We're using the value of 1e-8, which appears to be what | ||
| # Morin et al. (2021) used in their PSMC analysis | ||
| # (the default value), but I'm not sure, and this is not | ||
| # well justified | ||
| _overall_recombination_rate = 1e-8 | ||
| _recombination_rate = { | ||
| "1": _overall_recombination_rate, | ||
| "2": _overall_recombination_rate, | ||
| "3": _overall_recombination_rate, | ||
| "4": _overall_recombination_rate, | ||
| "5": _overall_recombination_rate, | ||
| "6": _overall_recombination_rate, | ||
| "7": _overall_recombination_rate, | ||
| "8": _overall_recombination_rate, | ||
| "9": _overall_recombination_rate, | ||
| "10": _overall_recombination_rate, | ||
| "11": _overall_recombination_rate, | ||
| "12": _overall_recombination_rate, | ||
| "13": _overall_recombination_rate, | ||
| "14": _overall_recombination_rate, | ||
| "15": _overall_recombination_rate, | ||
| "16": _overall_recombination_rate, | ||
| "17": _overall_recombination_rate, | ||
| "18": _overall_recombination_rate, | ||
| "19": _overall_recombination_rate, | ||
| "20": _overall_recombination_rate, | ||
| "21": _overall_recombination_rate, | ||
| "X": _overall_recombination_rate, | ||
| } | ||
|
|
||
| # Genome-wide average mutation rate is estimated by Robinson et al. (2022) | ||
| # by using divergence from two closely related species: harbor porpoise | ||
| # (Phocoena phocoena) and Indo-Pacific finless porpoise (Neophocaena phocaenoides). | ||
| # Using these two species and a range of assumptions results in a range of | ||
| # plausible estimates depicted in Fig S12 in the paper. | ||
| # Eventually, the representative value used in most analyses in the paper was | ||
| # 5.83e-9, which is on the high side of the range, to take into account previous | ||
| # higher estimates of the mutation rate, cited by Morin et al. (2021). | ||
| _overall_mutation_rate = 5.83e-9 | ||
|
|
||
| _mutation_rate = { | ||
| "1": _overall_mutation_rate, | ||
| "2": _overall_mutation_rate, | ||
| "3": _overall_mutation_rate, | ||
| "4": _overall_mutation_rate, | ||
| "5": _overall_mutation_rate, | ||
| "6": _overall_mutation_rate, | ||
| "7": _overall_mutation_rate, | ||
| "8": _overall_mutation_rate, | ||
| "9": _overall_mutation_rate, | ||
| "10": _overall_mutation_rate, | ||
| "11": _overall_mutation_rate, | ||
| "12": _overall_mutation_rate, | ||
| "13": _overall_mutation_rate, | ||
| "14": _overall_mutation_rate, | ||
| "15": _overall_mutation_rate, | ||
| "16": _overall_mutation_rate, | ||
| "17": _overall_mutation_rate, | ||
| "18": _overall_mutation_rate, | ||
| "19": _overall_mutation_rate, | ||
| "20": _overall_mutation_rate, | ||
| "21": _overall_mutation_rate, | ||
| "X": _overall_mutation_rate, | ||
| } | ||
|
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||
| _genome = stdpopsim.Genome.from_data( | ||
| genome_data.data, | ||
| recombination_rate=_recombination_rate, | ||
| mutation_rate=_mutation_rate, | ||
| ploidy=_ploidy, | ||
| # [ Implementers: please insert citations for the papers you are basing | ||
| # the estimates for recombination and mutation rates. The assembly | ||
| # citation is optional and can be deleted if not needed.] | ||
| citations=[ | ||
| stdpopsim.Citation( | ||
| author="Morin et al.", | ||
| year=2021, | ||
| doi="https://doi.org/10.1111/1755-0998.13284", | ||
| reasons={stdpopsim.CiteReason.ASSEMBLY}, | ||
| ), | ||
| stdpopsim.Citation( | ||
| author="Morin et al.", | ||
| year=2021, | ||
| doi="https://doi.org/10.1111/1755-0998.13284", | ||
| reasons={stdpopsim.CiteReason.REC_RATE}, | ||
| ), | ||
| stdpopsim.Citation( | ||
| author="Robinson et al.", | ||
| year=2022, | ||
| doi="https://doi.org/10.1126/science.abm1742", | ||
| reasons={stdpopsim.CiteReason.MUT_RATE}, | ||
| ), | ||
| ], | ||
| ) | ||
|
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||
| _species = stdpopsim.Species( | ||
| id="PhoSin", | ||
| ensembl_id="phocoena_sinus", | ||
| name="Phocoena sinus", | ||
| common_name="Vaquita", | ||
| genome=_genome, | ||
| # Robinson et al. (2022) and Morin et al. (2021) assumed an average | ||
| # generation time of 11.9 years in their analyses/calibrations. | ||
| # They cite Taylor et al. (2007) as a primary source. | ||
| # Table 1 in that paper specifies estimates of generation | ||
| # times for 58 cetacean species. It seems like the value selected was | ||
| # the one inferred for the sister species of harbor porpoise (Phocoena | ||
| # phocoena). The value estimated for Vaquita is slightly smaller (11.4), | ||
| # but maybe it reflects a recent reducion in generation time (???) | ||
| generation_time=11.9, | ||
| # Demographic models inferred for Vaquita by Morin et al. (2021) and | ||
| # Robinson et al. (2022) typically estimate small Ne of 2,000 - 5,000 | ||
| # in the past 500,000 years, likely followed by some sharp bottleneck. | ||
| # We selected as a representative Ne a value of 3500, which is also | ||
| # consistent with the average Ne inferred in the 2-epoch model of | ||
| # Robinson et al. (2022) | ||
| population_size=3500, | ||
| citations=[ | ||
| stdpopsim.Citation( | ||
| author="Robinson et al.", | ||
| year=2022, | ||
| doi="https://doi.org/10.1126/science.abm1742", | ||
| reasons={stdpopsim.CiteReason.POP_SIZE}, | ||
| ), | ||
| stdpopsim.Citation( | ||
| author="Robinson et al.", | ||
| year=2022, | ||
| doi="https://doi.org/10.1126/science.abm1742", | ||
| reasons={stdpopsim.CiteReason.GEN_TIME}, | ||
| ), | ||
| stdpopsim.Citation( | ||
| author="Taylor et al.", | ||
| year=2007, | ||
| doi="https://aquadocs.org/handle/1834/41281", | ||
| reasons={stdpopsim.CiteReason.GEN_TIME}, | ||
| ), | ||
| ], | ||
| ) | ||
|
|
||
| stdpopsim.register_species(_species) |